Fischer was detained at the international airport in this city just outside of Tokyo last Tuesday after trying to board a flight for Manila, Philippines.
Immigration officials, speaking on condition of anonymity, confirmed that Fischer, 61, has been held in their custody since, and said he is being processed for deportation. They refused to give further details, but said he could appeal their decision.
They said they did not know how long the deportation process would take.
A request by The Associated Press to meet with Fischer was denied by the airport immigration office, which cited "privacy concerns."
Fischer, believed by many to be the greatest chess player ever, has lived in seclusion and semi-secrecy for decades. It remains unclear where he considers home, but after he was taken into custody, friends here said he frequently traveled, staying for short durations in Japan, the Philippines, Germany and other countries.
He was believed to have been in Japan since about April.
Miyoko Watai, a member of the Japan Chess Association and a friend of Fischer, said the chess legend did not know that his passport had been revoked when he tried to leave Japan last week. She indicated that Fischer intends to appeal any effort to deport him.
Fischer became the U.S. chess champion at age 14, and a grandmaster at 15.
He became an icon in the United States when he defeated Soviet world champion Boris Spassky in a series of games in Reykjavik, Iceland. The games, in 1972, came at the height of the Cold War and were hailed in the United States as a major victory.
His hero status quickly faded amid his increasingly bizarre behavior, however. He lost his title as world champion in 1978 and then largely vanished from the public eye.
Fischer is wanted in the United States for playing a rematch against Spassky in Yugoslavia in 1992. Yugoslavia was under international sanctions at the time, and U.S. citizens were banned from doing business there.
Fischer won the match, and more than $3 million in prize money.
Over the years, Fischer gave occasional interviews with a radio station in the Philippines, often digressing into anti-Semitic rants and accusing American officials of hounding him.
He praised the Sept. 11 terrorist attacks, saying America should be "wiped out," and described Jews as "thieving, lying bastards." His mother was Jewish.
He also announced he had abandoned chess in 1996 and launched a new version in Argentina, "Fischerandom," a computerized shuffler that randomly distributes chess pieces on the back row of the board at the start of each game.
Fischer claimed it would bring the fun back into the game and rid it of cheats.
Alexander Roshal, of the Russian Chess Federation and chief editor of the chess magazine 64, said he had "mixed emotions" about the former champion.
"On the one hand, Fischer is a tough, notorious and quarrelsome person, but on the other hand he is a chess genius and contributed so much for the development of chess," said Roshal. "He is a pathologically perverted anti-Semite, which is strange knowing his origin, and I suspect he is not appreciated in America. But on the other hand, he has done so much good for the country and was the only American to defeat the Soviet grandmaster."
Former U.S. champion Alexander Ivanov of Newton, Mass., who followed the Reykjavik matches from the Soviet Union at age 16, said Fischer "was ahead of his time by about 15 years."
Watai, a longtime friend of Fischer's, said he could be "like a child."
"Chess had been his whole life, so he was sheltered from the world in some ways," she said. "Once he made up his mind, he would never change it, no matter what anyone said. That didn't always make people happy."
His emergence in Japan is not a complete surprise.
Fischer had been rumored to be living in Japan and was said to have frequented a Tokyo chess club. It is not clear how long he had been in the country.
"He came here often for short stays," said Watai. "He also traveled to the Philippines, Germany, Switzerland and many places."
American officials had apparently been following his recent movements.
Ferdinand Sampol, Philippine airport immigration chief, said the U.S. Embassy in Manila alerted immigration last week that Fischer might try to enter the country.
"But there was no request to exclude or remove him from the Philippines," he said.
Fischer is believed to have last visited the Philippines in 2003.
Filipino grandmaster Eugene Torre, another old friend, said Fischer had been planning to seek asylum in Switzerland, and was caught off guard by the arrest.
"Poor Bobby," he said.